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Quality control criteria and number of markers failing each criterion expressed as a percentage of the total 625,995 SNPs
| Category | Quality criterion | Proportion of rejected SNPs |
|---|---|---|
| Hardy–Weinberg equilibrium | P ≤ 0.001 | 3.6% |
| Completeness among individuals | ≤ 0.95 | 5.0% |
| Minor allele frequency | < 0.01 | 25.0% |
| Remaining SNPs | 431,249 (69% of all SNPs) |
Some markers failed more than one of the quality criteria
